Biomarker for barrett&#39;s oesophagus

ABSTRACT

The present invention, relates to the use of TFF3 in the diagnosis and detection of Barrett&#39;s Oesophagus using non-invasive, non-endoscopic methods.

RELATED APPLICATIONS

This application is a continuation of U.S. Pat. No. 9,632,099, filed onFeb. 7, 2014, entitled, “Biomarker for Barrett's Oesophagus” which iscontinuation of U.S. Pat. No. 8,709,736, filed Jul. 9, 2010, entitled“Biomarker for Barrett's Oesophagus,” which claims priority to GB0920014.8, filed Nov. 13, 2009, each of which are incorporated byreference in their entirety for all purposes.

FIELD OF THE INVENTION

The present invention relates to the diagnostic methods and compositionsfor use in the same. More particularly, the invention related to the useof TFF3 in the diagnosis and detection of Barrett's Oesophagus usingnon-invasive, non-endoscopic methods.

BACKGROUND OF THE INVENTION

Oesophageal adenocarcinoma is increasing rapidly in western countries[1, 2] and patients usually present late with locally advanced diseaseleading to a dismal overall 5 year survival rate of 13% [3]. Barrett'soesophagus (BE), as defined by intestinal metaplasia, is the majoridentified risk factor for this cancer [4] and in those patients withoesophageal adenocarcinoma at presentation 90% have evidence of BEfollowing shrinkage of the tumor post-chemotherapy [5]. However, becausethe majority (86%) of adenocarcinomas present de novo [6] (without priordiagnosis of BE) it is likely that a large number of BE patients remainundiagnosed in the population. This idea is supported by the highprevalence of BE (7-25% for segments of any length and 0.7-7% for longsegment Barrett's) in asymptomatic patients who agreed to have ascreening upper GI endoscopy when attending for colonoscopy in the US[7-9]. In keeping with these overall figures the prevalence of BE of anylength was reported to be between 1 and 8% in all corners to endoscopy(reviewed in Pera, 2003 [10]). The only population prevalence dataavailable suggests that BE is present in 1.6% of the general Swedishpopulation [11].

Evidence from non-randomized retrospective studies demonstrated animprovement in 5-year actuarial survival from 13-43% to 62-100% inpatients with surveillance-detected oesophageal adenocarcinomas [12-18].These data suggest a potential benefit for early detection although leadtime bias needs to be accounted for. Rapid advances in endoscopictechnologies (reviewed by Reddymasu and Sharma [19]) as well as thedevelopment of chemoprevention strategies [20, 21] afford theopportunity to improve patients' outcomes if disease is detected early.

Thus, identification of undiagnosed BE patients should ultimately reducemortality from oesophageal adenocarcinoma. To attain this objective,population-based screening for Barrett's is required. However there aremajor feasibility and cost implications for the wide-scale applicationof screening using the gold standard endoscopy [22].

Since the architecture of the tissue is well conserved, H&E slides maybe reviewed by an expert gastrointestinal histopathologist butmorphology alone is often not sufficient to diagnose BE and is open tosubjectivity.

Novel screening strategies might include symptom nomograms, wirelesscapsule endoscopy and balloon cytology [23-25] but these have not yetbeen demonstrated to be sufficiently sensitive and specific for clinicaluse [26-28]. Recently, a study using a wireless video capsule attachedto a string, allowed a more careful examination of the oesophagus andeliminated previous a major imaging drawback of fast oesophageal transittime with a reported sensitivity of 93.5% [29]. However, this approachdoes not permit a pathological diagnosis or the potential forimplementing risk stratification using biomarkers.

Neither the British Society of Gastroenterology nor the AmericanGastroenterology Association currently recommend endoscopic screeningfor BE [22, 57] (recommendations grade C and B respectively, both basedon cohort and case control studies). However, both professionalorganizations agree that surveillance is in order once BE is diagnosed.However, for surveillance to be of use, all Barrett's patients,symptomatic or asymptomatic would need to be diagnosed. This suggestspopulation screening for BE may be recommended if a cost effective testcould be developed. It is a problem that there is currently no suitablecost effective test available. The present invention seeks to overcomeproblem(s) in the art.

BRIEF SUMMARY OF THE INVENTION

The present invention relates to the use of TFF3 in the diagnosis anddetection of Barrett's Oesophagus using non-invasive, non-endoscopicmethods. In particular, the methods of the present invention relate toscreening for Barrett's oesophagus (BE) in a subject comprisingobtaining a sample of cells from the cellular surface of the oesophagusof a subject, determining the presence of Trefoil factor 3 (TFF3) insaid sample of cells, wherein the presence of said TFF3 is indicative ofsaid subject having BE. In particular embodiments, this non-invasivescreening method employs cells taken from the subject wherein the cellsare a mixed population of cells taken from the cellular surface of theoesophagus. More specifically, the oesophageal cells comprise cells fromthe oesophagus and gastric mucosa cells. It is a particular feature ofthe present invention that the method does not require the use of anendoscopy or other biopsy but is instead a non-invasive sampling methodthat simply uses the cells from an oesophageal brushing, preferably anon-endoscopic oesophageal brushing. Moreover, it is an advantage of thepresent invention that the screening method can be performed and yieldpositive results even in the absence of the subject having BE lesions.

In the methods described herein the cells are collected in anon-invasive manner using a swallowable device comprising an abrasivematerial capable of collecting cells from the surface of the oesophagus.For example, such a device comprises a capsule sponge that can bescraped along the oesophageal tract and withdrawn and the cellsdeposited thereon analysed for the presence of TFF3 protein orexpression of TFF3. The methods described herein have a superiorspecificity and sensitivity as compared to the methods known in the art.For example, use of the TFF3 as a diagnostic marker for diagnosis of BEproduces at least about high specificity of 80% and about 65%respectively. More particularly, the method has a specificity andsensitivity for diagnosis of BE of about 94% and about 78% respectively.

The methods of the invention may further be used to differentiate amixed population of alimentary tract cells obtained from a subjectsuspected of having Barrett's oesophagus (BE) comprising determining thepresence or expression of TFF3 on the surface of said cells, wherein thepresence of TFF3 on the surface of any of the cells in the mixedpopulation of cells identifies said cells as being from a BE lesion inthe alimentary tract.

The TFF3 may be detected using any method known in the art.Advantageously, the presence of TFF3 is detected in an immunoassay usingan antibody specific for TFF3. In other embodiments, the TFF3 isdetected on the surface of the cells using an immunohistochemicaldetection method. The diagnosis of BE may be further confirmed bystaining the cells with an Alcian Blue stain which is known to stainpositive for cells taken from BE lesions.

BRIEF DESCRIPTION OF SEVERAL VIEWS OF THE DRAWINGS

FIG. 1: Venn diagram of the number genes identified by analyses 1, 2 andgenes common to the two microarray analyses. Analysis 1 and 2 yielded 24and 93 putative targets respectively. A total of 14 genes common to bothanalyses were validated further. (BE: Barrett's oesophagus, NE: normaloesophagus, NS: normal stomach, CG: chronic gastritis, GIM: gastricintestinal metaplasia).

FIG. 2: mRNA expression of the putative genes identified. The Y axisrepresents the −ΔCt (defined as −(Ct_(target)−Ct_(GRAPH))). The starsindicate statistical significance by one-way ANOVA (*p=0.0339 and**p=0.0012); only genes whose expression was significantly increased inBE compared to NE and GM are marked on this graph. In both cases, thegenes were statistically upregulated in BE compared to NE and GC. Inaddition, AGR2, ATP7B, FBP1, FMO5, FOXA3, GOLPH2, LYZ, RNAase4 and TFF1are statistically upregulated in BE (Barrett's oesophagus) and GC(gastric cardia) compared to NE (normal oesophagus).

FIG. 3: Immunohistochemistry for TFF3 and DDC. Representativeimmunohistochemistry (×100) of TFF3 in the positive control duodenum, NE(normal oesophagus), BE (Barrett's oesophagus), GM (gastric mucosa).

FIG. 4: Cumulative score for TFF3 in normal oesophagus, Barrett'soesophagus, stomach and duodenum. TFF3 is statistically over-expressedin BE (Barrett's oesophagus) compared to NE (normal oesophagus) and GM(gastric mucosa, p<0.0001).

FIG. 5: Expression of DDC in prostate cancer, used as positive control,and in a positive Barrett's oesophagus biopsy (×100 and ×400magnification).

FIG. 6A-6D: Representative haematoxilin and eosin and TFF3 staining of acapsule specimen collected from a Barrett's patients (×100 and ×400magnification). The black arrow indicates the typical circularappearance of TFF3 positivity and the red arrow indicates secreted TFF3at the apical border of the Barrett's cells.

FIG. 7A-7B shows: Cytosponge within the capsule and expanded (A) andrepresentative picture of positive TFF3 staining in a sample from apatient with BE (B).

FIG. 8 shows a diagram.

FIG. 9A-9C shows a timeline.

FIG. 10 shows a summary chart.

DETAILED DESCRIPTION OF THE INVENTION

We disclose TFF3 as a biomarker for BE. We have demonstrated for thefirst time that microarray analysis can be directly applied to theclinic in the context of BE. TFF3 was identified as one of a number ofcandidate markers by selection from a large volume of publicallyavailable DNA microarray data. The inventors demonstrated that it wasover-expressed in BE compared to adjacent normal tissues at the RNA andprotein level. We disclose its use in a novel minimally invasive,non-endoscopic screening strategy.

The invention provides improved diagnostic accuracy via identificationand validation of biomarker(s) that have the ability to clearlydistinguish between cells from BE, normal gastric and squamousoesophageal cells since the preferred capsule-sponge mode of collectionsamples cells from the stomach to the oro-pharynx. The biomarkerprovided is highly specific which has the advantage of minimising costsince in a screening programme, patients with a positive capsule testwould need to undergo endoscopy to verify the diagnosis and allow formultiple biopsies to be performed to exclude dysplasia.

Trefoil factors are mucin-associated petides thought to be involved inmultiple biological functions including repair of the mucosa throughenhancement of restitution (mucosal repair by cell migration) andmodulation of stem cells differentiation as well as interaction withmucins and modulation of the mucosal immune response [40-43]. In thegastrointestinal tract, TFF1 and 2 are mainly expressed by the gastricepithelium [42] while TFF3 is expressed by the intestine and intestinalmetaplasia of the stomach and oesophagus [44, 45]. TFF3 expression hasbeen demonstrated to be increased by gastro-oesophageal refluxdisease[45], and transient overexpression of the homeodomain proteinCDX2 [46], linking its expression to the development of BE.Interestingly, there have been a number of publications concerning thedevelopment of novel cytological methods using TFF3 to detect thyroidfollicular carcinomas [47, 48] and it has been suggested that TFF3 couldalso be detected in the serum of patients with high-grade endometrialcarcinomas [49]. It might therefore be possible to develop a serum basedassay to screen for BE using TFF3 as a marker.

Dopadecarboxylase metabolizes 3,4-dihydroxyphenylalanine (DOPA) todopamine and 5-hydroxytryptophan to serotonin [50]. Overexpression ofDDC is also a feature of a number of malignancies ranging fromretinoblastomas [51, 52] to small cell lung cancers [53], prostatecancers [54] and gastric cancers with peritoneal disseminations [55]. Inmost of these tumor types, an effort has been made to use DDCdiagnostically using PCR techniques in biopsies [54, 56] or cytologicalspecimens [55]. DDC may therefore be of interest as a biomarker formalignant conversion in Barrett's and due to the poorimmunohistochemistry staining a PCR based assay may be more applicable.

An advantage of this novel capsule sponge test is that it can beperformed in primary care. Since the TFF3 analysis presented here relieson standard immunohistochemical techniques it is an objective test thatwould be readily applicable to clinical pathology laboratories in a costeffective manner. Furthermore, in the future other assays could beapplied to these sponge samples such as PCR based assays to determinegene expression levels of multiple biomarkers or DNA based assays todetermine methylation status or loss of heterozygosity. Suchmethodologies might increase the price of the test but may also beinformative with regards to the risk of progression to cancer. Thetypical circumscribed appearance of TFF3 positivity and the strength ofthe staining make it particularly suited for automation thus potentiallyfurther reducing the cost of a screening program incorporating thismethodology.

For such a BE screening test, it is advantageous to have a highspecificity to avoid calling patients for unnecessary endoscopies withthe inherent generation of anxiety, high costs and risks of an invasiveprocedure that this would entail. With TFF3 we obtained a very highspecificity of 94% and an adequate sensitivity of 78%. It is unlikelyfor a single marker to provide both a high sensitivity and specificity.It is reasonable to accept that a device like the capsule sponge, whilesampling from the entire surface of the mucosa, will only collect cellsthat detached. Small foci of IM, yielding TFF3 positivity, may bemissed, explaining the sensitivity of 78%.

TFF3

In the search for a robust marker, the inventors undertook an intensivegenetic and biochemical analysis. Initially, the inventors analysed datarelating to approximately 54,000 genes. This initial screening effortwas based on a combination of various available data sets. The aim wasto identify candidate markers which might be increased in Barrett'soesophagus but would not show an increase in non-Barrett's tissue suchas gastric cardia or squamous oesophagus. This was an impartial analysiswith no bias or choice introduced in selection of candidates. In otherwords, this could be regarded as a genome wide search. Promisingcandidates were taken forward for validation.

An initial validation step was based on PCR amplification. Candidatespassing this test were taken forward.

A further step towards validation was to obtain antibodies recognisingthe candidates. Those candidates which could be recognised by antibodieswere taken forward for further validation.

A further validation step was undertaken by tissue staining. Thoseantibodies capable of showing a differentiation/discrimination weretaken forward for further validation.

Antibody staining was then validated on samples of cells which wereobtained non-specifically (for example by use of a capsule spongesampling technique).

The culmination of the design and application of each of the rigorousscreening steps devised and implemented by the inventors was theidentification of TFF3 as a robust marker for Barrett's oesophagus.

The initial genetic screening approach supplied 14 candidates. Thevarious validation steps narrowed these 14 candidates down to only 2candidates. One of these showed only deep tissue staining together withinfrequent or rare staining patterns and behaved as a very poor marker.The conclusion of the screening and multiple validation steps was thatTFF3 was the only consistent and robust marker for use in detection ofBarrett's oesophagus in this setting.

TFF3 showed an initial sensitivity of 79% and an initial specificity of94%. These findings are demonstrated in the examples section.

Furthermore, although not powered to determine accuracy of the test as aprimary outcome measure, when non-specific sampling techniques such asthe cyto-sponge sampling technique were used, TFF3 demonstrated asensitivity of 90% and a specificity of 94% for detection of Barrett'soesophagus.

It is an advantage of the invention that these levels of sensitivity andspecificity are so high. Moreover, it was an unexpected finding of theinventors at such high levels of specificity would be associated withTFF3.

Suitably sensitivity is 79% or more. Suitably sensitivity is 90% ormore.

Suitably specificity is 94% or more.

Sample

Suitably the sample comprises cells from the subject of interest.Suitably the sample comprises oesophagal cells from the subject ofinterest. Suitably the sample is non-endoscopic ie. suitably the sampleis obtained without the use of an endoscope. Endoscopic sampling is aninvasive technique. Furthermore, endoscopic sampling is a targetedtechnique where biopsies are taken at intervals along the oesophagus, orwhere lesions are visually identified by the operator and specificallytargeted for biopsy. Suitably the invention does not involve endoscopicsamples such as endoscopic biopsies.

Prior art techniques for detecting Barrett's oesophagus have typicallyinvolved a targeted sample such as an endoscopic biopsy together with aproliferation marker such as MCM2. This essentially asks the questionwhether, in a specifically chosen sample obtained by a skilledendoscopic operator, there are any cells which are proliferating (e.g.dys-regulated). Although this is clearly useful, it is not suitable forpopulation screening due to the expensive, time consuming and invasivenature of the targeted endoscopic sampling.

A key principle of the invention is to provide a marker which isspecific for Barrett's oesophagus. The marker is specific for Barrett'soesophagus in the sense of not naturally occurring in unrelated tissuessuch as normal squamous oesophagus, or gastric cardia (stomach). Thus,by providing a marker with these specific characteristics, the inventionadvantageously provides a marker targeted to detection of Barrett'soesophagus cells. In this way, the invention advantageously avoids theneed for targeted sample collection. Thus, the invention advantageouslyinvolves samples obtained by non-targeted sample collection such assampling the entire surface of the oesophagus rather than only targetingareas of suspected lesions (Barrett's).

Thus, suitably sample does not comprise an endoscopic biopsy.

Suitably the sample may comprise oesophical brushings or surface cells.Oesophagal brushings may be obtained using an endoscope or by othermeans; suitably when the sample comprises oesophagal brushings they areobtained by non-endoscopic means.

Suitably the sample may comprise cells sampled from the entireoesophagal lumen.

Suitably the sample may comprise both oesophagal and non-oesophagalcells.

Suitably the sample may comprise oesophagal cells together with gastriccardia cells.

Most suitably, the sample may comprise cells collected using a capsulesponge type sampling technique.

Especially suitable sampling techniques are described in the examplessection.

Examples of suitable samples include oesophagal brushings (whetherendoscopically or non-endoscopically obtained), samples obtained viaballoon cytology, samples obtained via capsule sponge sampling. Mostsuitably, a sample comprises cells obtained via capsule sponge sampling.It can therefore be appreciated that TFF3 possesses certain propertieswhich make it advantageous as a biomarker for Barrett's oesophagus.

Firstly, TFF3 exhibits luminal surface expression. This means that thesample to be analysed need only be collected from the surface of theoesophagal lumen. This advantageously avoids the need for a biopsy suchas an endoscopic biopsy. Moreover, this advantageously avoids the needto preserve tissue architecture in the sample being analysed.

A further advantage of TFF3 is that it is able to differentiate betweenthe oesophagal lumen and the gastric mucosa. Specifically, TFF3 is notexpressed in the gastric mucosa (e.g. gastric cardia/stomach). This hasa specific advantage that if cells of the gastric mucosa are included inthe sample, then TFF3 is still able to function as a robust biomarkerfor Barrett's. This is because TFF3 is not expressed in gastric mucosacells, and therefore no false positives occur even when the samplecomprises cells of the gastric mucosa. Thus, this capacity fordifferentiation is another robust advantage of TFF3 in the presentinvention. This property is in particularly sharp contrast to othermembers of the TFF3 family of proteins since TFF3 appears to be uniqueamongst TFF proteins in not identifying cells of the gastric mucosa.

Thus it can be appreciated that the choice of TFF3 by the inventorsprovides a degree of specificity which has not yet been provided in anyprior art approach to screening for Barrett's oesophagus. The presentinventors were the first to actively seek, and to successfully provide,a marker capable of such focused discrimination. Moreover, samplingtechniques in the prior art have been confined to oesophagus. Thus, theinventors are the first to have identified the utility of a markerhaving the properties disclosed herein, as well as being the only onesto have identified such a marker.

A non-endoscopic capsule sponge device which has been approved by theMedical Health Regulatory Agency (Ref n# CI/2007/0053) in the UK may beused for sample collection. A pilot study demonstrated that this deviceis acceptable to patients and could be used in primary care [30], [31].The device consists of a polyurethane sponge, contained within a gelatincapsule, which is attached to a string. The capsule is swallowed anddissolves within the stomach after 3-5 minutes. The sponge can then beretrieved by pulling on the string. Initial studies were performed usinga cell monolayer stained with a proliferation marker mcm2. This gave asuboptimal sensitivity and specificity of 67.5% and 67.4% respectivelyand sample heterogeneity meant that the whole sample had to be processedand analyzed for this single biomarker. More recently, we have processedthe cytological specimen to a pellet which can then be embedded inparaffin thus preserving the tissue architecture. This can then undergohistological assessment and in addition, multiple immunohistochemicalmarkers may be used on a single sample [31]. Thus, mode of samplecollection is particularly suitable for use in the present invention.

Mode of Detection

The marker may be detected by any suitable means known in the art. Forexample, the marker may be detected using nucleic acid based techniquessuch as RNA analysis.

Suitably, the marker is detected at the protein level.

Most suitably, the marker is detected using antibodies such as anti-TFF3antibodies.

It is an advantage of the invention that quantitative levels ofexpression need not be determined. It is an advantage of the inventionthat mere presence/absence of the marker is sufficient to aid thediagnosis of Barrett's oesophagus.

Thus it is an advantage of the invention that a qualitative measurement(e.g. simple presence or absence) is sufficient to aid the diagnosiswithout needing to resort to quantitative measurement.

It is an advantage of the invention that controls or reference samplesare not necessary, since it is possible to work the invention scoringonly a simple presence or absence of TFF3.

It is an advantage of the invention that TFF3 may be analysed on itsown. In other words, combinations with other markers are not necessaryfor performance of the invention.

The methodology used for marker identification ensured high specificitysince we identified the best discriminators between BE and NE and GM butnot necessarily sensitivity because the sample size of the microarrayswas not high enough. Current screening programs for prostate (prostateserum antigen), cervical (Papanicolaou test) and colon cancer (fecaloccult blood test (FOBT)) have accepted sensitivities of 30-96%respectively and specificities of 77-100% respectively [59-61]. Thepositive predictive value of PSA for prostate cancer and of FOBT forcolon cancer is 47% and 2.2-17.7% respectively [59, 60]. It maytherefore be desirable to identify additional markers that, used inconjunction of TFF3, would offer a high sensitivity without loss ofspecificity. Naturally, if the skilled worker wishes to analyse markersother than TFF3 in parallel, then this does not adversely effect theinvention. For example, it may be desired to use Alcian Blue staining inparallel with TFF3 analysis. Alcian blue stains goblet cells andtypically stains the same cells as express TFF3. Alcian blue may be usedto confirm Barrett's oesophagus in biopsies. Thus, in one embodiment,the invention relates to analysing a sample for the expression of TFF3,and analysing said sample using Alcian blue staining.

The invention provides non-endoscopic screening biomarkers for Barrett'soesophagus. These find application in microarray analysis and in theclinic. In particular the invention finds application in populationscreening such as non-invasive screening for Barrett's.

Barrett's oesophagus (BE) predisposes to oesophageal adenocarcinoma butthe majority of patients are undiagnosed. A non-endoscopic cytologicalscreening device, called a capsule sponge, makes population-basedscreening for BE a feasible option. However, due to the mixed cellpopulation retrieved by the capsule sponge, biomarkers specific for BEare required. The present invention provides the TFF3 biomarker which isspecific for BE, in particular specific for BE amongst the heterogeneouscells in samples such as those collected by capsule sponge sampling. Inother words, TFF3 is an excellent marker for BE screening since it isexpressed at the luminal surface of BE but not in adjacent tissue typesand may be applied to a non-endoscopic screening device.

Further Applications

The invention may relate to use of TFF3 as a BE biomarker when used incombination with non-endoscopic sampling.

TFF3 has the advantage of luminal surface expression and differentialexpression with the gastric mucosa.

The invention may relate to use of TFF3 as biomarker for BE wheresensitivity and specificity are at least 79% and 94% respectively. Theinventors were surprised by the unexpectedly high levels of specificityand sensitivity shown for TFF3.

The present invention provides methods of aiding the diagnosis ofBarrett's oesophagus or Barrett's associated dysplasia in a subject,said method comprising sampling the cellular surface of the oesophagusof said subject, and assaying the cells for the presence of TFF3,wherein detection of TFF3 indicates increased likelihood of the presenceof Barrett's or Barrett's associated dysplasia. In particular, thesampling is efficient because it is not directed to a particular sitewithin the oesophagus but instead the sample of cells is taken acrossthe entire surface of the oesophagus. This has the advantage of avoidingmore invasive sampling techniques such as biopsy collection techniqueswhich penetrate below the surface of the oesophagus.

In addition to the detection of TFF3, the cells may also be monitored todetermine the presence of other markers of BE such as those markers thatare indicative of brush border proteins such as villin or moesin, mucingenes, brush border enzymes such as alkaline phosphatase, homeobox genessuch as Cdx1 and/or Cdx2, cytokeratins such as CK8/18 for columnarcells, or any marker known to be differentially expressed in Barrett'sversus normal oesophageal surface cells.

Preferably in addition to TFF3, the additional marker may be selectedfrom the group consisting of proliferation markers such as Ki67 and Mcmproteins, proliferation and DNA damage markers such as PCNA, cyclinssuch as cyclin D and/or cyclin A, abnormal p53, loss of p16, aneuploidyor any marker known to correlate with the degree of dysplasia. Morepreferably the marker is Mcm2 or Cyclin A.

In the methods the invention the sampling of the cellular surface of theoesophagus comprises the steps of

(i) introducing a swallowable device comprising abrasive materialcapable of collecting cells from the surface of the oesophagus into thesubject, (ii) retrieving said device by withdrawal through theoesophagus, and (iii) collecting the cells from the device.

Preferably step (i) comprises introducing a swallowable devicecomprising abrasive material capable of collecting cells from thesurface of the oesophagus into the subject's stomach.

In another aspect, the invention provides a method as described abovefurther comprising analysing the chromosomal composition of the cells,wherein detection of abnormal karyotype indicates an increasedlikelihood of dysplasia.

In another aspect, the invention provides a kit comprising a swallowabledevice comprising abrasive material capable of collecting cells from thesurface of the oesophagus, together with printed instructions for itsuse in detection of TFF3 to diagnose Barrett's oesophagus or Barrett'sassociated dysplasia.

In another aspect, the invention provides a kit as described abovefurther comprising a local anaesthetic. Preferably said localanaesthetic is a spray or lozenge, preferably a spray.

In another aspect, the invention provides a kit as described abovefurther comprising a container for receiving said swallowable deviceafter withdrawal, said container having a quantity of preservative fluidtherein. Preferably the container is a watertight container. Preferablythe preservative fluid is a cell preparation fluid. Preferably saidfluid is thin preparation fluid for production of slides for examinationof the sampled cells.

In another aspect, the invention provides a kit as described abovewherein said device comprises a capsule sponge.

In another aspect, the invention provides a kit as described abovewherein said swallowable device comprises withdrawal means such asstring.

In another aspect, the invention provides a kit as described abovefurther comprising a device for severing said withdrawal means.Preferably said device comprises a blade or scissors.

In the kit there also may be a container for administering drinkablefluid, such as water, to the subject. The kit may also contain a localanaesthetic spray or lozenge to facilitate the deliver and sampling ofthe oesophagus cells using the sponge device.

In another aspect, the kit invention provides a kit as described abovefurther comprising reagents for use in the detection of at least onemarker selected from the group consisting of brush border proteins suchas villin or moesin, mucin genes, brush border enzymes such as alkalinephosphatase, homeobox genes such as Cdx1 and/or Cdx2, cytokeratins suchas CK8/18 for columnar cells, or any marker known to be differentiallyexpressed in Barrett's versus normal oesophageal surface cells.

Barrett's Oesophagus can occur without dysplasia. Approximately 1% ofpatients with Barrett's oesophagus will develop dysplasia each year. Atany given time, approximately 20% of patients with Barrett's oesophaguswill have dysplasia. Cancer such as adenocarcinoma develops fromdysplasia and is regarded as one extreme form of dysplasia, even thoughpathologically the conditions clearly differ. It is desirable to obtainan early diagnosis of adenocarcinoma and the present invention isconcerned with such detection and diagnosis of a single progressivedisease state that has recognisable discrete stages. These stagescomprise Barrett's oesophagus, Barrett's oesophagus associated dysplasiaincluding adenocarcinoma, which arises therefrom.

In these diagnostic methods, the cells are sampled from the surface ofthe oesophagus using a swallowable abrasive material, which material isretrieved from the patient and from which the cells are subsequentlyseparated for analysis to determine the presence of TFF3. Preferablysubstantially the entire surface of the oesophagus is sampled,preferably the entire surface. In the present invention, there is noneed to focus only on Barretts oesophagus lesions as the inventors havefound that the presence of TFF3 is associated only with BE and as suchTFF3 can be used to specifically diagnose whether a mixed population ofcells obtained from the entire surface of the oesophagus have thereincells that are from BE lesions.

By abrasive is meant that the material is capable of removing cells fromthe internal surface of the oesophagus. Clearly, since this is meant foruse in a subject's oesophagus, ‘abrasive’ must be interpreted in thelight of the application. In the context of the present invention theterm ‘abrasive’ has the meaning given above, which can be tested bypassing the material through the oesophagus in an appropriateamount/configuration and examining it to determine whether cells havebeen removed from the oesophagus.

The material used in the collection device must be sufficiently abrasiveto sample any dysplastic cells present in the oesophagus. Preferably thematerial is sufficiently abrasive to sample any Barrett's oradenocarcinoma cells present. In a most preferred embodiment, preferablythe material is sufficiently abrasive to be capable of sampling thewhole oesophagus ie. so that some squamous cells are collected togetherwith any Barrett's and/or columnar and/or adenocarcinoma cells which maybe present. This is advantageous because squamous cells are moredifficult to remove than dysplastic cells and so their sampling providesa control to the operator such that if normal squamous cells are removedby the material then the chances of having not sampled the cells ofinterest such as Barrett's or dysplastic cells (if present), which areeasier to remove than normal squamous cells, is correspondingly small.

Preferably the swallowable abrasive material is expandable. In thisembodiment, preferably the abrasive material is of a smaller size whenswallowed than when withdrawn. An expandable material may be simply aresilient material compressed such that when released from compressionit will expand again back to a size approximating its uncompressed size.Alternatively it may be a material which expands e.g. upon taking upaqueous fluid to a final size exceeding its original size.

In other words, preferably the material of the device expands, swells,inflates or otherwise increases in size between swallowing andwithdrawal. Preferably the device is auto-expandable ie. does notrequire further intervention between swallowing and expansion.Preferably the device is not inflatable. Preferably the device expandsby unfolding, unfurling, uncoiling or otherwise growing in sizefollowing removal of restraint after swallowing. Preferably the materialof the device is compressible and reverts a size approximating itsuncompressed size following swallowing. Preferably the device isconstructed from a compressed material which is releasably restrained ina compressed state. Preferably the material is released from restraintafter swallowing, allowing expansion of the device/material beforewithdrawal.

Preferably the device comprises compressible material which iscompressed into capsule form. Preferably the compressible material is inthe form of sponge material.

Preferably the compressed sponge is at least partially surrounded by asoluble and/or digestible coat such as a capsule coat. Preferably thesponge is indigestible. Preferably the capsule coat is at leastpartially formed from gelatin. Preferably the capsule coat is fullyformed from gelatin.

In one embodiment it may be desirable to make the whole device out ofdigestible material to increase safety in case of a device becoming lostin the subject. Naturally the abrasive material would need to bedigested at a slower rate than the capsule and the cord would need to besimilarly slowly digested. Preferably the abrasive material isnon-digestible. Preferably the cord is non-digestible.

Preferably the abrasive material comprises polyurethane, preferablypolyurethane sponge.

Preferably the device is a capsule sponge. As will be apparent from thespecification, a capsule sponge is a device comprising compressiblesponge as the abrasive material, which sponge is compressed into acapsule shape, which capsule shaped compressed sponge is preferablyreversibly restrained in its compressed state by at least a partial coatof soluble and/or digestible material such as gelatine. Preferably thedevice is a capsule sponge as supplied by Francois Venter at MedicalResearch Council, South Africa. Preferably the device is a capsulesponge as manufactured by Medical Wire and Equipment (MWE), Corsham,Wiltshire, UK.

Preferably the sample does not comprise endoscopically collectedmaterial. Preferably the sample does not comprise endoscopic biopsy.Preferably the sample does not comprise endoscopic brushings.

It is a feature of the invention that the sampling is not directed e.g.visually directed to any particular part of the oesophagus but ratherthe sponge is scraped along the entire surface of the oesophagus andobtains a heterogeneous sample of cells from the tract. It is a furtheradvantage of the invention that a greater proportion of the surface ofthe oesophagus is sampled than is achieved by prior art techniques suchas endoscopic biopsy (which samples approximately 1% of the surface) orendoscopic brushing. Preferably at least 10% of the oesophageal surfaceis sampled, preferably at least 20%, preferably at least 30%, preferablyat least 40%, preferably at least 50%, preferably at least 60%,preferably at least 70%, preferably at least 80%, preferably at least90%. In a most preferred embodiment, preferably substantially the entireoesophagus is sampled, preferably the whole inner lumen of theoesophagus is sampled. This applies equally to the in vitro sample evenwhen the method of the invention does not include collection of thesample.

The invention will now be described by way of examples, which areintended to be illustrative and are not intended to limit the scope ofthe appended claims. Reference is made to the following figures.

Certain Abbreviations are used, including BE Barrett's oesophagus, CGChronic gastritis, GC Gastric cardia, GIM Gastric intestinal metaplasia,GM Gastric mucosa, IM Intestinal metaplasia, NE Normal oesophagus, NSNormal stomach.

EXAMPLES

Overview

We hypothesized that biomarkers for BE can be identified by combiningand re-analyzing a number of previously published upper gastrointestinalmicroarray datasets. In this way we identify putative biomarkers from acombinatorial in silico analysis and then perform validation studies onindependent samples at the RNA and protein level before finally applyingany candidates to samples from a capsule sponge collected from anindependent cohort of Barrett's patients and healthy controls.

Three publically available microarray datasets were used to identifyputative biomarkers present in BE but absent from squamous oesophagus(NE) and gastric mucosa (GM). Validation was performed by QPCR (n=10each of NE, BE, GM) and immunohistochemistry (NE n=20, BE n=21, GM n=24,duodenum n=18).

2/14 genes identified, dopa-decarboxylase (DDC) and Trefoil Factor 3(TFF3), were confirmed by QPCR to be upregulated in BE compared to NE(p<0.01) and GM (p<0.01 and p<0.05 respectively). Immunohistochemistryconfirmed that DDC protein expression was restricted to BE but wasconfined to <1% of the cells within the crypt compartment. TFF3 proteinwas expressed to high levels at the luminal surface of BE compared toabsent expression in NE and GM (p<0.001).

The biomarker was then prospectively evaluated on capsule spongespecimens from 47 BE patients and 99 healthy controls. Using the capsulesponge 36/46 BE patients (1 inadequate sample) and 6/96 controls werepositive for TFF3 giving a sensitivity of 78% and a specificity of 94%.

Example 1: Identification of Putative Targets

We used a strategy involving three microarray datasets to screen forcandidate genes that were specifically expressed in BE. Twenty fourgenes from analysis 1 (Hao/Boussioutas) were found to be statisticallyoverexpressed in BE (log₂ ratio>2) compared to NE (log₂ ratio<1) and GM(log₂<1). Using the same log₂ ratio comparisons 93 genes were identifiedfrom analysis 2 (Greenawalt/Boussioutas), (FIG. 1).

Microarray Analysis

The invention is based in part on a substantial leap forward in thetranslation of high throughput laboratory results into an assay that canbe used in the clinic. The microarray experiments were not designedspecifically to identify markers distinguishing between BE, NE and GMand to our knowledge no dataset including normal oesophagus, Barrett'soesophagus and normal gastric mucosa exists. Furthermore, the microarrayplatform by of Hao et al. [32] was different from the platform used byBoussioutas et al. [33] and Greenawalt et al. [34]. This explains thelower number of candidates identified in the first (Hao-Greenawalt;n=33) compared with the second analysis (Boussioutas-Greenawalt; n=111)(see below). However, very stringent statistical criteria were set toreduce the effect of these shortfalls which also reduced the number ofputative targets.

A search of the literature (PubMed) and public gene expressionmicroarray databases (GEO, Stanford Microarray Database) was performedto identify microarray datasets pertaining to gene expression patternsin IM-containing BE, NE (normal squamous oesophagus) and gastric mucosa(normal stomach (NS), chronic gastritis (CG) and gastric IM (GIM)).These tissues were selected since they will sampled by the capsulesponge.

CG and GIM were chosen to represent upper GI inflammation andHelicobacter-induced IM respectively, which may be present in thescreened population and need to be distinguished from BE. Threedatasets, detailed in Table 1, were selected for analysis based on thefollowing criteria: a) data was generated from more than 5 samples perrelevant tissue type and; b) the arrays used contained >10000 cDNA oroligonucleotide probes. All three microarray studies involved thehybridisation of differentially labelled test and reference cDNA to aspotted cDNA array, and data from all three studies were available inthe form of normalised test:reference hybridisation signal intensityratios. Different analyses were performed to generate a single gene list(FIG. 1). Analysis 1: Hao et al. [32] (15 NE and 14 BE) was analyzed,using a parametric test (Welch t-test) with Bonferroni correction, toidentify genes which were differentially expressed between the twogroups and whose expression was significantly upregulated in BE (log₂ratio>2) compared to NE, (p<0.0001). This list was then used tointerrogate Boussioutas et al. [33] (57 gastric mucosa samples (GM)comprising NS, CG and GIM) for genes that were under-expressed in GM(<1). Analysis 2: Greenawalt et al. [34] (39 NE and 26 BE) was analyzedin a similar fashion to dataset 1 to produce a set of genes with log₂ratios BE>2, NE<1 and GM<1 (from Boussioutas et al. [33]). Data analysiswas done using GeneSpring GX version 7.3 (Agilent, Palo Alto, Calif.,USA). Genes common to both analyses were selected and ranked in order ofstatistical significance and enrichment in BE for subsequent validation.

TABLE 1 microarray datasets selected for analysis Specimens ArrayReference Normalisation Source of data Hao 15 Normal Spotted CommercialIntensity- Stanford microarray [32] oesophagus cDNA human dependentdatabase 14 Barrett's array RNA (http://genome- oesophagus (42,000www5.stanford.edu) spots) Boussioutas 8 Normal Spotted Pool of 11 LOWESSGEO Accession [33] stomach cDNA normal normalisation GSE2669 27 Chronicarray gastric gastritis (11,500 specimen 22 Gastric IM spots) Greenawalt39 Normal Spotted Pool of 11 LOWESS ArrayExpress ID [34] oesophagus cDNAcell lines normalisation E-MEXP-692 26 Barrett's array oesophagus(11,500 spots)

It was found that 14 genes (table 3 and FIG. 1) were common to bothanalyses.

TABLE 3 Putative biomarkers, primer sequences and PCR conditionsAccession Forward Reverse Annealing Name Symbol n# primer primer T° C.Anterior AGR2 NM_006408 TTGTCCTCCTCAATC GCAGGTTCGTAAGCA 53 gradient 2TGGTTTATG TAGAGAC (SEQ ID NO. 1) (SEQ ID NO. 2) ATPase, Cu2+ ATP7BNM_000053.2 ACAAAGCACTAACCC ATATTCAAGACGCAA 53 transporting, AAAGAGACGACTTACAATG polypeptide (SEQ ID NO. 3) (SEQ ID No. 4) Death-associatedDAPK1 NM_004938 AACTACGAATTTGAG GATCCAGGGATGCTG 53 protein kinase-1GATGAATACTTC CAAAC (SEQ ID NO. 5) (SEQ ID NO. 6) M-Dopa DDC NM_000790CTTCGCCTACTTCCC CTTTGGTAGTTCCAG 55 decarboxylase CACTG CATCTTCC(SEQ ID NO. 7) (SEQ ID NO. 8) Fructose-1,6- FBP1 NM_000507CACTGAGTACATCCA CTTCTTGTTAGCGGG 57 biphosphate GAGGAAG GTACAGdecarboxylase (SEQ ID NO. 9) (SEQ ID NO. 10) Flavin containing FMO5NM_001461.1 GGACAGGCGACACTA CCTTTCAAAGCAGAC 53 monooxygenase ACAGGAGGTTCC (SEQ ID NO. 11) (SEQ ID NO. 12) Forkhead box A3 FOXA3NM_004497.2 TGCTGCCTCGACCAC AGTGAAATAGGGTGT 56 CAC GGAGGAAG(SEQ ID NO. 13) (SEQ ID NO. 14) Fucosyl- FUT4 NM_002033.2 N/A* N/A* N/Atransferase 4 golgi GOL NM_177937.1 AGTGTGAGGAGCGAA TGTCTGGGACTTGCT 53phosphoprotein 2 PH2 TAGAAGAG GTTACC (SEQ ID NO. 15) (SEQ ID NO. 16)lysozyme (renal LYZ NM_000239.1 GACCTAGCAGTCAAC CCATTCCCAATCTTT 53amyloidosis) ATGAAGG TCAGAGTTC (SEQ ID NO. 17) (SEQ ID No. 18)phospholipase PLCL2 NM_015184.2 CCATCAAGGAAGTGA ATATATGACGGAAAA 56C-like 2 GAACAGG CGCACAATC (SEQ ID NO. 19) (SEQ ID NO. 20) ribonuclease,RNAse4 NM_194430 GCAGAGGACCCATTC CGCAGGAATCGCTGG 57 RNase A ATTGC TACfamily, 4 (SEQ ID NO. 21) (SEQ ID No. 22) Trefoil factor 1 TFF1NM_003225 CCCCGTGAAAGACAG CGTCGATGGTATTAG 53 AATTGTG GATAGAAGC(SEQ ID NO. 23) (SEQ ID NO. 24) Trefoil factor 3 TFF3 NM_003226.2TCTGGGAGCTTGACA GGATTGTTTGCTTGG 56 AAGGC GGAAGG (SEQ ID NO. 25)(SEQ ID NO. 26) *N/A: qPCR analysis was not performed since no suitablepositive control could be identified

It is interesting to note that only 2 out of 14 targets were validatedby qPCR and in most cases this was because the expression level of theputative markers was similar in GM (cardia) and BE. This suggests thatthe expression profile of the cardia is closer to BE than normal gastricmucosa, chronic gastritis and intestinal metaplasia of the cardia. Ithas previously been demonstrated that the kinome [38] and the expressionprofile [39] of BE have strong similarities to that of gastric cardia.

Example 2: Validation of Targets

Human Specimens

Patients undergoing upper GI endoscopy were recruited to this biomarkerstudy from Addenbrooke's Hospital following approval by the LocalResearch Ethics Committee. All patients with BE, had an endoscopicallyvisible columnar lined segment of more than 3 cm and a histopathologicaldiagnosis of specialized intestinal metaplasia. For NE samples weretaken 2 cm above the z-line in patients with BE and 2 cm above thegastro-oesophageal junction (GOJ) in patients without BE who wereundergoing symptomatic evaluation as part of the routine surveillanceservice.

The microarray targets were validated using real-time PCR (RT-PCR) in 10samples from each of BE, NE (5 from Barrett's patients and 5 fromnon-Barrett's patients with a normal oesophagus) and 10 GM samples(collected from the cardia of Barrett's patients, table 2). The cardiawas defined as 1 cm below the upper border of the gastric folds at thelower oesophagus in non-Barrett's patients. A frozen section from eachsnap frozen Barrett's specimen was analyzed by a histopathologist toconfirm the presence of IM prior to RNA extraction.

The protein expression of putative biomarkers validated by RT-PCR wasconfirmed by immunohistochemistry on paraffin embedded section from anindependent cohort of 21 non-dysplastic BE, 20 NE, 24 GM and 18non-inflamed duodenum specimens which were used as a controlcolumnar-lined tissue containing goblet cells (table 2).

TABLE 2 Clinical characteristics of cohorts Age Length BE Number (medianM:F (cm of patients [95% C1]) ratio [95% CI]) Real time PCR Normaloesophagus 10 62 [56-59] 1.5:1  8.3 [6-10]*  Barrett's oesophagus 10 65[61-68] 2:1 Gastric mucosa 10 63 [56-69] 1.5:1  ImmunohistochemistryNormal oesophagus 20 59 [49-71] 0.8:1  4.3 [3.2-5.3] Barrett'soesophagus 21 70 [63-78] 2:1 Gastric mucosa 24 62 [57-66] 1.5:1 Duodenum 18 58 [24-75] 1:1 Capsule sponge Control patients 99 60 [58-62]1:1 6.5 [4.9-7.4] Known Barrett's 47 64 [60-67] 3:1 *indicate that thelength of the BE samples used for RT-PCR is statistically longer thanthose for immunohistochemistry (p < 0.01)

RNA Extraction Real-Time PCR

Total RNA from biopsies was extracted by using Trizol (Invitrogen). 1 μgof RNA was reverse transcribed using SuperScript II reversetranscriptase kit (Invitrogen, Paisley, UK) in 20 μL of total reactionsolution. The primers used are listed in Table 2. Positive controls wereidentified for each primer pair using a screen of 25 cells lines fromdifferent tissue origins. Quantitative PCR was performed on 2 μL of cDNAwith the SYBR Green JumpStart Taq Readymix according to manufacturer'sinstructions (Sigma-Aldrich, Dorset, UK). PCR consisted of 40 cycles of94° C. denaturation (15 s), 51-57° C. annealing (30 s; see table 1) andextension (30 s). The cycle threshold Ct was determined for each sample,and the average Ct of triplicate samples was calculated. The expressionof each gene relative to Glyceraldehyde-3-Phosphate Dehydrogenase(GAPDH) was determined as ΔCt. A melt curve was constructed for eachprimer.

Immunohistochemistry

5 μm sections were de-paraffinised in xylene and rehydrated in ethanol.Antigen retrieval was performed in microwave MicroMed TT-Mega(Milestone, Sorisole, Italy) in 0.01 M citrate buffer pH 6.4. Thestaining procedure was performed using the Dako EnVision™+ System.Briefly, non-specific binding was blocked by incubation in 5% BSA inTBS-Tween 0.05% for 1 h and endogenous peroxidises were blocked with thehydrogen peroxide provided with the kit. Tissue sections were incubatedwith the primary antibody, either mouse anti-TFF3 (R&D Systems EuropeLtd, Abington, UK) or mouse anti-DDC (Protos Biotech Corporation, NewYork, USA) in 1% BSA in TBS-Tween 0.05% for 1 h at room temperature. Thelabelled polymer provided with the kit was then applied for 45 minfollowed by DAB substrate (DakoCytomation Ltd) for 10 min. Sections werecounterstained with haematoxylin. A negative control was performed byomission of the primary antibody. Since the capsule sponge samplessurface epithelium, quantification of immunohistochemical staining wasrestricted to the 4 top most layers of the mucosa. A mean of the extentand intensity was generated for each biopsy, reviewed at highmagnification (×400), to generate an overall score for each slide. Theintensity score was: 0 if absent, 1 for weak, 2 for medium and 3 forstrong staining. The extent of staining was scored 1 for focal (1 focusof positive cells), 2 for multifocal (2 or more foci of positive, cells)and 3 for extensive (whole biopsy stained) staining.

Analysis

The increased expression in BE compared to NE and GM was first confirmedat the mRNA level by real-time PCR in 10 histopathologically verifiedendoscopic biopsies from each tissue type. A suitable positive controlcould not be identified for FUT4 despite evaluating 3 primer pairsacross 25 cells lines from different tissues. Validation of this targetgene was therefore not taken any further. The expression of DAPK1 andPLCL2 was not statistically different between any groups. Most targets(AGR2, ATP7B, FBP1, FMO5, FOXA3, GOLPH2, LYZ, RNAase4 and TFF1) werestatistically increased in BE compared to NE but were similar to GM(FIG. 2). However, both Dopa decarboxylase (DDC) and Trefoil factor 3(TFF3) were statistically over-expressed in BE compared to NE (p<0.001and p<0.01 respectively) and GM (p<0.01 and p<0.05 respectively).

Since the capsule sponge specifically samples the uppermost layers ofthe mucosa, we then went on to validate the expression of TFF3 and DDCin paraffin-embedded section to address the epithelial localization ofthe antigen. TFF3 was expressed to high levels in BE compared to NE andGM both at the luminal surface and deeper within the tissue (FIGS. 3 and4, p<0.001). TFF3 was therefore applicable to the capsule sponge whichsamples the surface layers of the gastric cardia and oesophagus. Incontrast, DDC expression was only seen in 4/19 patients with BE and wasabsent in adjacent tissues (NE or GM) as expected. In the positive BEsamples, DDC expression was very weak, limited to a small cluster ofcells (less than 8) and localized towards the bottom of the crypts (FIG.5).

Example 3: TFF3 Expression in Samples Collected with the Capsule Sponge

Since TFF3 fulfilled the necessary criteria, in that expression wasrestricted to the luminal surface of BE with no expression seen ingastric or normal squamous oesophageal tissues this was taken forward tothe prospective capsule sponge screening study. TFF3 expression inspecimens from 46 histologically confirmed BE patients were compared to99 patients without BE.

Capsule Sponge Specimens

Following approval by the Cambridge Local Research Ethics Committee, 29patients with known long-segment BE and 99 control patients (table 2),whose diagnosis was verified by endoscopy, were recruited. Only patientswith a segment 3 cm were recruited to avoid erroneous diagnoses ofhiatus hernia. Control patients were selected on the basis that they hadreflux symptoms sufficient to require a prescription of acid-suppressantfor a minimum of 3 months over the last 5 years but without diagnosis ofBE. The patients were invited to attend a clinic at which they swallowedthe sponge with a bolus of water and the capsule was left in place for 5minutes before retrieval in preservative solution (SurePath, BurlingtonN.C., USA) as previously described [30].

Processing of the Capsule Sponge Specimens

Samples were left in preservative solution for a minimum of 1 hour. Thesamples were incubated for 30 minutes in Cytolyt® solution (Cytyccorporation), washed twice in PBS and pelleted at 1000 RPM for 5minutes. The resulting pellet was re-suspended in 500 μL of plasma andthrombin (Diagnostic reagents, Oxford, UK) was then added in 10 μLincrements until a clot formed. The clot was then placed in formalin for24 h prior to processing into a paraffin block. The entire sample wascut in 5 μm sections to provide 20 slides. The first slide and everytenth slide were stained with H&E. Two sections representative of thewhole sample, 10 slides apart, were stained for TFF3 as described above.A slide was scored positive for TFF3 if any cell was stained for TFF3.

Statistical Analysis

A Kruskal-Wallis one-way analysis of variance by ranks was performed toanalyse differences in mRNA expression and expression of TFF3 at theluminal surface between the three groups using Prism (GraphPadSoftware). Specific differences were identified using a Dunn's posttest. Microarray analysis was performed as described above.

One sample from a known Barrett's patient had a low cell yield and wasexcluded from the analysis. The staining was very intense (FIG. 6) and adichotomous score (staining present or not) was used to maximizespecificity. 36 out 46 patients and 6 out of 99 control patients had acapsule sponge specimen positive for TFF3. A sensitivity of 78% (95% CI64-89), specificity of 94% (95% CI 87-98) and a correct proportion ofsamples diagnosed of 89% (95% CI 83-94) were obtained.

We have demonstrated identification and use of a clinically relevantbiomarker through the use of microarray data and careful validation. Thebiomarker identified using such an approach may be used in conjunctionwith the capsule sponge test to provide a cost-effective and acceptablescreening test for BE.

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Trager C, Vernby A, Kullman A, et al. mRNAs of tyrosine    hydroxylase and dopa decarboxylase but not of GD2 synthase are    specific for neuroblastoma minimal disease and predicts outcome for    children with high-risk disease when measured at diagnosis. Int J    Cancer 2008.-   57. Wang K K, Sampliner R E. Updated Guidelines 2008 for the    Diagnosis, Surveillance and Therapy of Barrett's Esophagus Am J    Gastroenterol 2008; 103:788-97.-   58. Donaldson L. On the State of Public Health: Annual Report of the    Chief Medical Officer 2007. 2008;    http://www.dh.gov.uk/en/Publicationsandstatistics/Publications/Annual    Reports/DH_086 176: Accessed 20 Jan. 2009.-   59. Bunting P S. Screening for prostate cancer with    prostate-specific antigen: beware the biases. Clin Chim Acta 2002;    315(1-2):71-97.-   60. Towler B, Irwig L, Glasziou P, et al. A systematic review of the    effects of screening for colorectal cancer using the faecal occult    blood test, hemoccult. Bmj 1998; 317(7158):559-65.-   61. Nanda K, McCrory D C, Myers E R, et al. Accuracy of the    Papanicolaou test in screening for and follow-up of cervical    cytologic abnormalities: a systematic review. Ann Intern Med 2000;    132(10):810-9.

Example 4: BEST2: Evaluation of a Non-Endoscopic ImmunocytologicalDevice (Cytosponge) for Barrett's Esophagus Screening Via a Case-ControlStudy and a Screening Trial in Primary Care

Background

Incidence rates of oesophageal adenocarcinoma (AC) have increased 6 foldin the last 30 years [1] and the 5 year survival remains less than 14%[2]. For these reasons, both Cancer Research UK and the Chief MedicalOfficer have highlighted this disease as a strategic priority andrecommended that research should be supported to explore minimallyinvasive screening tests [3]. The ability to detect BE is a criticalscreening question because this is the precursor for oesophagealadenocarcinoma. Hitherto the utility of screening for BE has beenquestionable given the lack of treatment options. However, there hasbeen rapid advancement in technologies such as endoscopic mucosalresection and radiofrequency ablation with randomised controlled trialevidence to support their efficacy [4, 5]. In addition, chemopreventionmeasures are being evaluated in a large CRUK funded trial (AspECT).Therefore screening-detected cases of BE could potentially be coupled tointerventions to prevent AC thus avoiding the need for oesophagectomywhich has significant mortality and morbidity [2].

Any screening test needs to be simple, safe, precise, validated andacceptable to the population [6]. The current gold-standard endoscopicdiagnosis is invasive, technical and expensive. Development of ultrathintransnasal endoscopy may improve acceptability; however it remains aninvasive, expensive test requiring technical expertise [7, 8]. Wirelessvideo capsule endoscopy has a high sensitivity [9]; but is alsohigh-tech, expensive and does not permit tissue sampling. Previousattempts to develop non-endoscopic cytological screening tests, such asballoon cytology have failed [10].

Development of the Cytosponge Test and Pilot Data

We have developed an MHRA approved (CI/2007/0053) non-endoscopic devicecalled a Cytosponge to screen for BE (FIG. 1A). It consists of anexpandable, spherical mesh which is attached to a string and containedwithin a soluble capsule. 3-5 minutes after swallowing, the mesh can beretrieved by pulling on the string. After placing into preservativefluid the specimen is processed for biomarker evaluation (FIG. 1B). In acase:control study the most promising BE biomarkers were an antibodyraised against the proliferation marker Mcm2; and a mucin characteristicof the intestinal metaplastic phenotype TFF3 [11, 12]. Protein basedassays were chosen for their applicability to routine clinicaldiagnostic pathology laboratories.

Next we examined the feasibility and acceptability of using theCytosponge in primary care (www.beststudy.org.uk), [13, 14]. To date 491patients (mean age, 62 years with a M:F ratio of 0.8:1) with a historyof reflux disease have been recruited from 2,602 patients from 11practices giving an uptake of 18.9% in line with previous primary careendoscopic studies [15, 16]. Only 3/491(<0.01%) were unable to swallowthe device and there were no serious adverse events. Cytosponge resultswere compared with endoscopy as the gold-standard with a compliance of92%. In this population the prevalence of BE containing specializedintestinal metaplasia was 2.2%, in keeping with other non-UK populationdata [16-19]. Although not powered to determine accuracy of the test asa primary outcome measure, the Cytosponge test detected BE (TFF3) with asensitivity and specificity of 90% and 95% respectively. Hence, thispilot study has demonstrated that the Cytosponge is simple and safeenough to be applied to the primary care setting. Further data arerequired to validate the test and provide robust data on its precision.See FIG. 7.

Biomarkers for Risk Stratification

BE progresses to adenocarcinoma via a metaplasia-dysplasiaadenocarcinoma sequence at a rate of 0.6% per year [20]. Therefore, inorder to avoid placing an undue burden on endoscopic surveillance, theideal screening test should also risk stratify patients according totheir likelihood of progressing to AC. This is currently assessed by thehistopathological assessment of the degree of dysplasia on biopsies butmore objective molecular biomarkers are emerging.

DNA ploidy, p16 and p53 abnormalities are currently the best predictorsof cancer progression with a relative risk of up to 38.7 (95% CI10.8-138.5; p<0.001) [21, 22]. Whilst the assays employed for theseanalyses are highly technical, image cytometric analysis of ploidy [23,24] and immunohistochemical detection of p53 abnormalities are promising[25]. In addition, cyclin A and MCM2 detect >90% high grade andadenocarcinoma cases [12, 26]. Since these markers specifically detectepithelial cell surface abnormalities using routine immunohistochemistrythey are ideally suited to the Cytosponge. Finally, a panel of 8methylated genes assayed from paraffin embedded specimens have beenvalidated in a double blind study [27, 28].

Hypothesis

We hypothesise that the Cytosponge test could be used as a clinicalscreening test in primary care, which when coupled with appropriatebiomarkers could also diagnose the degree of dysplasia.

Proposed Design

A screening trial together with a Case:Control study will recruitpatients from three different populations in order to determine theperformance characteristics of the Cytosponge for diagnosing BE comparedwith endoscopy, including specificity (from controls) and sensitivity(from cases) and numbers needed to test (from the primary-care basedtrial). The project design was driven by the need to: a) maximise theinformation gained with regards to both diagnosis of BE and presence ofdysplasia and b) to avoid endoscoping individuals with a negativeCytosponge result who would otherwise not have sought medical care. Thedesign is summarised in FIG. 8.

1. Screening Trial: Primary Care

The primary clinical outcome measure for the screening trial will behistologically confirmed BE.

Setting and Practice Recruitment

2,500 individuals with symptomatic reflux will be identified and invitedto swallow the Cytosponge via the East of England (EoE) Primary CareResearch Network (PCRN). From the 20% acceptance rate in the BEST pilotstudy we would require a combined practice population of about 500,000people, from 55-60 practices which is possible via the EoE PCRN. Allinterested surgeries will be visited by the study staff to discuss thepurpose and logistics of the study including a video of a volunteerswallowing the Cytosponge.

Inclusion and Exclusion Criteria

Individuals 50-70 years of age who have required an anti-refluxprescription for >3 months over the past 5 years will be identified froma search of the electronic drug prescribing data base by the practicestaff. Patients who had upper GI endoscopy in the past year, those whoare known to have BE and individuals unable to give informed consentwill be excluded.

Appointment Process

The subject will provide demographic information which will be enteredby the study nurse using a custom-made database accessed via the web.Baseline information will be collected (weight, height, waist:hip ratio)and patients will complete a validated reflux questionnaire [29]. TheCytosponge will be administered by the study nurse. Following the testand whilst still in the surgery the subject will complete baselinepsychological measures (see section on QOL).

Patients with a positive test (defined on the basis of any TFF3positivity) will be invited for an endoscopy within 6 weeks. Any BEvisible endoscopically will be confirmed with biopsies for standardhistopathological evaluation. Further psychological questionnairemeasures will be sent by post at days 7 and 90.

A subgroup of individuals (1500 invited to recruit 1200 over theduration of the study) with a negative Cytosponge test will be offered arepeat test (either 1 or 2 years later) and as in the first screeningtest individuals testing positive will be endoscoped and psychologicalquestionnaires completed.

2. Case-Control Study Secondary Care

The primary clinical outcome measure for the case-control study will bepositive staining for TFF3.

Recruitment

500 individuals with known BE (cases) undergoing surveillance, includingthose referred for further evaluation and management of high gradedysplasia (HGD) will be recruited. 500 individuals referred by their GPfor an endoscopic evaluation of dyspepsia (controls) will also beinvited to attend. The timeline of the study is summarized in FIGS.9A-9C.

Inclusion and Exclusion Criteria

Any patient clinically fit for an endoscopy is eligible to take part.Individuals with dysphagia will be excluded. Patients must be able toprovide informed consent.

Appointment Process

Baseline demographic and symptom information will be collected asdescribed from the screening trial. After obtaining informed consent theCytosponge will be administered by the study nurse prior to theirclinically indicated endoscopy. Any newly endoscopically diagnosed BE inthe control arms will be biopsied as for the screening trial and thesepatients will be then be considered as cases. For patients undergoingsurveillance, biopsies will be taken according to the Seattle protocoland graded according to the Vienna classification system [30]. Prior tobiopsies, an endoscopically directed brushing of Barrett's mucosa willbe taken for biomarker evaluation to compare with the Cytospongespecimen as previously described [12, 26]. Psychological questionnairemeasures will be obtained at days 0, 7 and 90.

Sample Processing from Screening and Case Control Arms

All Cytosponge specimens will be processed as previously described [11]and evaluated for the Barrett's diagnostic biomarkers (TFF3) using aDAKO autostainer according to GCP standards. Samples will be scored in abinary fashion (positive or negative) as already optimised from thepilot study. A screener will identify areas of interest for the expertGI cytologist (M O′D) to verify.

Patients with a positive result for the Barrett's diagnostic biomarkerswill have additional sections cut for risk stratification biomarkers.Mcm2, cyclin A and TP53 can be performed on the DAKO autostainer. Theploidy analysis will be performed using image cytometry [23], (Lovatlaboratory) and methylation will be performed using methylation specificPCR [27], (Fitzgerald laboratory). The biomarkers will be scoredaccording to previously optimised protocols [11, 12, 23, 26]. These datawill be compared to the degree of dysplasia determined from endoscopicbiopsies.

Primary and Secondary Clinical Outcomes from Screening and Case ControlArms:

Primary Outcome:

-   -   Performance characteristics of the Cytosponge test for        diagnosing BE compared with endoscopy, including specificity        (from controls) and sensitivity (from cases) and numbers needed        to test (from the primary-care based screening trial).

Secondary Outcomes:

-   -   Differential sensitivity of screening BE with high-grade        dysplasia compared to non-dysplastic BE.    -   For patients with BE, (screened and surveillance patients) we        will determine the ability of Cytosponge biomarkers to risk        stratify patients in comparison with dysplasia grade obtained        from endoscopic biopsies.    -   Preliminary data on numbers needed to test to detect one case of        BE after an interval of one and two years following a negative        screen. These data will be key to determining the screening        frequency for future trials.    -   Logistics of high-throughput sample processing and automated        analysis of Cytosponge specimens for use in routine NHS or other        health care settings.    -   Recruitment rates and acceptability in the primary care-trial        will be determined and compared between different        socio-demographic groups.

Potential for Bolt-on Studies and Translational Research:

-   -   Surplus material from screening and surveillance populations        will be used for testing emerging biomarkers    -   Longer term (20 years), the incidence of oesophageal        adenocarcinoma in individuals with positive versus negative test        will be available through flagging with the ECRiC Eastern Cancer        Registry and Information Centre.    -   Opportunity to re-contact participants in the screening trial in        relation to other cancer prevention behavioural interventions        e.g. smoking cessation, obesity reduction or chemoprevention.

Sample Size Estimation:

The main goal is to obtain accurate estimates of the screeningparameters (sensitivity, specificity, positive predictive value andnumbers needed to screen to detect one case). We therefore aim toestimate specificity with 95% confidence intervals of approximately+/−1% and sensitivity with intervals of +/−2.5%. Where testing has beenconsidered (such as comparing Barrett's with and without high gradedysplasia, or comparing results at entry and 12 or 24 months later) wehave aimed for between 80% and 90% power. Details sample sizeconsiderations are available from Peter Sasieni on request.

Additional Information on Study Logistics:

A full-time study co-ordinator will be based in Cambridge and workclosely with the Cancer Prevention Trials Unit.

1) Screening Trial: Primary Care

Three full-time research nurses based in EoE will work in parallel torecruit participants. The NIHR primary care network is being approachedfor funding support for research nurses. Twice monthly endoscopy, inprimary-care associated units in proximity to the practices concerned,will be performed by a Joint Advisory Board (JAG) accredited upper GIendoscopist. Appointments will be made by a full-time study bookingclerk working with the study co-ordinator in Cambridge.

2) Case:Control Study: Secondary Care

The patients will be recruited form 3 tertiary referral centres(Cambridge, Nottingham and UCLH) with expertise in BE (over 700 patientsper year of which 135 have HGD). These centres all have research nurseswho will have dedicated time for this study (5 sessions per week).

Quality of Life and Economic Evaluations

To measure the impact of screening on psycho-social well-beingparticipants will complete the validated Impact of Events Scale and theShort Form STAI/TRAIT anxiety questionnaires before the test, 7 and 90days later. Health state utility data using the EQ-5D as recommended byNICE [31]) and resource use data (diagnostic and therapeutic endoscopy,anti-reflux medication, surgery) will be collected. This informationwill subsequently be used to populate a Markov process model to estimatethe cost per QALY from a UK perspective to compare to existing dataconcerning endoscopic screening for BE [32]. Funding is not required forthis part of the proposal. A parallel application will be made to theNIHR to fund quality of life and health economic studies. See FIG. 10.

Preparation, staining and reading of slides from the Cytosponge will bedone blinded to the route by which the patient was recruited (screening,case, potential control) and to any endoscopy findings. Similarly, BEhistology will be evaluated blinded to the reason for endoscopy(surveillance or triage of a positive screen). Interim analyses will beperformed at the end of the first and second year of the study.

The data will be analysed using standard techniques for screeningstudies. In the screening trial adjustments will be made for the lack ofendoscopy both in those who screen negative and more particularly inthose who screen positive but subsequently fail to comply withrecommended follow-up. A detailed statistical analysis plan will beproduced in conjunction with PS before the data are examined.Exploratory analyses will explore factors (such as ages, sex andobesity) affecting specificity and disease prevalence in the screeningtrial.

Clinical Governance

The Cancer Prevention Clinical Trials Unit will ensure clinicalgovernance standards are met and will advise on practical issues. TheTFF3 biomarker assays will be performed in clinical histopathologicallaboratories to GCP standards. All clinical decisions concerninginterventions for BE associated dysplasia will be made on the basis ofthe histopathological grading of the endoscopic biopsies according tostandard clinical practice without reference to biomarker data.

An advisory board will meet annually during the course of the study to:oversee and advise, serve as a dissemination vehicle to otherresearchers and policy makers and to serve as a ‘springboard’ forsubsequent epidemiological and clinical collaborations.

Anticipated Use of Study Results to Inform Clinical Decision Making

Increasing public awareness and an increasing incidence of AC mean thatit is timely to conduct work to inform policy decisions about a nationalBE screening programme. In the future the results from this study couldlead on to a RCT to compare the effects of screening, coupled withendoscopic treatment for those individuals diagnosed with high risk BE,compared with no screening on mortality form AC.

REFERENCES

-   1. Brown, L M, Devesa, S S, and Chow, W H, Incidence of    adenocarcinoma of the esophagus among white Americans by sex, stage,    and age. (2008) J Natl Cancer Inst 100(16), 1184-1187.-   2. Medical Research Council Oesophageal Cancer Working Group,    Surgical resection with or without preoperative chemotherapy in    oesophageal cancer: a randomised controlled trial. (2002) Lancet    359(9319), 1727-1733.-   3. Donaldson, L, Chapter 6: A pathological concern: Understanding    the rise in oesophageal cancer. (2007) Annual Report of the Chief    Medical Officer,    http://www.dh.gov.uk/en/Publicationsandstatistics/Publications/AnnualReports/DH_0861    76.-   4. Shaheen, N J, Sharma, P, Overholt, B F, et al., Radiofrequency    ablation in Barrett's esophagus with dysplasia. (2009) N Engl J Med    360(22), 2277-2288.-   5. Pouw, R E, Wirths, K, Eisendrath, P, et al., Efficacy of    Radiofrequency Ablation Combined With Endoscopic Resection for    Barrett's Esophagus With Early Neoplasia. (2009) Clin Gastroenterol    Hepatol.-   6. UK National Screening Commitee, Criteria for appraising the    viability, effectiveness and appropriateness of a screening    programme. (2009) http://www.screening.nhs.uk/criteria.-   7. Saeian, K, Staff, D M, Vasilopoulos, S, et al., Unsedated    transnasal endoscopy accurately detects Barrett's metaplasia and    dysplasia. (2002) Gastrointest Endosc 56(4), 472-478.-   8. Dumortier, J, Napoleon, B, Hedelius, F, et al., Unsedated    transnasal EGD in daily practice: results with 1100 consecutive    patients. (2003) Gastrointest Endosc 57(2), 198-204.-   9. Ramirez, F C, Akins, R, and Shaukat, M, Screening of Barrett's    esophagus with string-capsule endoscopy: a prospective blinded study    of 100 consecutive patients using histology as the criterion    standard. (2008) Gastrointestinal Endoscopy 68(1), 25-31.-   10. Fennerty, M B, DiTomasso, J, Morales, T G, et al., Screening for    Barrett's esophagus by balloon cytology. (1995) Am J Gastroenterol    90(8), 1230-1232.-   11. Lao-Sirieix, P, Boussioutas, A, Kadri, S R, et al.,    Non-endoscopic screening biomarkers for Barrett's oesophagus: from    microarray analysis to the clinic. (2009) Gut 58(11), 1451-1459.-   12. Sirieix, P, O'Donovan, M, Brown, J, et al., Surface expression    of mini chromosome maintenance proteins provides a novel method for    detecting patients at risk for developing adeocarcinoma in Barrett's    oesophagus. (2003) Clin Cancer Res.-   13. Kadri, S R, Debiram, I, Lao-Sirieix, P, et al., A pilot    feasibility study of screening for Barrett's esophagus with a novel    non-endoscopic capsule sponge device in a primary care    setting. (2009) Gastroenterology 136 (Suppl 1), T1877.-   14. Kadri, S R, Lao-Sirieix, P, O'Donovan, M, et al., Non-endoscopic    screening for Barrett's oesophagus in the community. (In    preparation).-   15. Wong, A, Lovat, L, Burnham, R W, et al., Large-scale prospective    study reveals novel risk factors for Barrett's oesophagus. (2007)    Gut 56(supp II), A8.-   16. Ronkainen, J, Aro, P, Storskrubb, T, et al., Prevalence of    Barrett's esophagus in the general population: an endoscopic    study. (2005) Gastroenterology 129(6), 1825-1831.-   17. Gerson, L B, Shetler, K, and Triadafilopoulos, G, Prevalence of    Barrett's esophagus in asymptomatic individuals. (2002)    Gastroenterology 123(2), 461-467.-   18. Rex, D K, Cummings, O W, Shaw, M, et al., Screening for    Barrett's esophagus in colonoscopy patients with and without    heartburn. (2003) Gastroenterology 125(6), 1670-1677.-   19. Ward, E M, Wolfsen, H C, Achem, S R, et al., Barrett's Esophagus    Is Common in Older Men and Women Undergoing Screening Colonoscopy    Regardless of Reflux Symptoms. (2006) The American Journal of    Gastroenterology 101(1), 12-17.-   20. Sikkema, M, de Jonge, P J, Steyerberg, E W, et al., Risk of    Esophageal Adenocarcinoma and Mortality in Patients With Barrett's    Esophagus: A Systematic Review and Meta-Analysis. (2009) Clin    Gastroenterol Hepatol.-   21. Galipeau, P C, Li, X, Blount, P L, et al., NSAIDs modulate    CDKN2A, TP53, and DNA content risk for progression to esophageal    adenocarcinoma. (2007) PLoS Med 4(2), e67.-   22. Chao, D L, Sanchez, C A, Galipeau, P C, et al., Cell    Proliferation, Cell Cycle Abnormalities, and Cancer Outcome in    Patients with Barrett's Esophagus: A Long-term Prospective    Study. (2008) Clin Cancer Res 14(21), 6988-6995.-   23. Dunn, J M, Rabinovitch, P S, Oukrif, D, et al., Comparison of    image cytometry and flow cytometry for detection of DNA ploidy    abnormalities in Barrett's oesophagus. (2009) Biochemical Society    Transactions In press.-   24. Fang, M, Lew, E, Klein, M, et al., DNA abnormalities as marker    of risk for progression of Barrett's esophagus to adenocarcinoma:    image cytometric DNA analysis in formalin-fixed tissues. (2004) Am J    Gastroenterol 99(10), 1887-1894.-   25. Murray, L, Sedo, A, Scott, M, et al., TP53 and progression from    Barrett's metaplasia to oesophageal adenocarcinoma in a UK    population cohort. (2006) Gut 55(10), 1390-1397.-   26. Lao-Sirieix, P, Lovat, L, and Fitzgerald, R C, Cyclin A    immunocytology as a risk stratification tool for Barrett's esophagus    surveillance. (2007) Clin Cancer Res 13(2 Pt 1), 659-665.-   27. 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TABLE 1 microarray datasets selected for analysis Specimens ArrayReference Normalisation Source of data Hao, 15 Normal Spotted CommercialIntensity- Stanford microarray 2006³³ oesophagus cDNA human dependentdatabase 14 Barrett's array RNA (http://genome- oesophagus (42,000www5.stanford.edu) spots) Boussioutas, 8 Normal Spotted Pool of 11LOWESS GEO Accession 2003³⁴ stomach cDNA normal normalisation GSE2669 27Chronic array gastric gastritis (11,500 specimen 22 Gastric IM spots)Greenawalt, 39 Normal Spotted Pool of 11 LOWESS ArrayExpress ID 2007³⁵oesophagus cDNA cell lines normalisation E-MEXP-692 26 Barrett's arrayoesophagus (11,500 spots)

TABLE 2 Clinical characteristics of cohorts Age Length BE Number (medianM:F (cm of patients [95% CI]) ratio [95% CI]) Real time PCR Normaloesophagus 10 62 [56-59] 1.5:1  8.3 [6-10]* Barrett's oesophagus 10 65[61-68] 2:1 Gastric mucosa 10 63 [56-69] 1.5:1  ImmunohistochemistryNormal oesophagus 20 59 [49-71] 0.8:1  4.3 [3.2-5.3] Barrett'soesophagus 21 70 [63-78] 2:1 Gastric mucosa 24 62 [57-66] 1.5:1 Duodenum 18 58 [24-75] 1:1 Capsule sponge Control patients 99 60 [58-62]1:1 5.7 [4.3-7.1] Known Barrett's 29 64 [60-67] 3:1 *indicate that thelength of the BE samples used for RT-PCR is statistically longer thanthose for immunohistochemistry (p < 0.01)

TABLE 3 Putative biomarkers, primer sequences and PCR conditionsAccession Annealing Name Symbol number Forward primer Reverse primer T°C. Anterior AGR2 NM_006408 TTGTCCTCCTCAATC GCAGGTTCGTAAGCA 53 gradient 2TGGTTTATG TAGAGAC (SEQ ID NO. 1) (SEQ ID No. 2) ATPase, Cu2+ ATP7BNM_000053.2 ACAAAGCACTAACCC ATATTCAAGACGCAA 53 transporting, β AAAGAGACGACTTACAATG polypeptide (SEQ ID NO. 3) (SEQ ID NO. 4) Death- DAPK1NM_004938 AACTACGAATTTGAG GATCCAGGGATGCTG 53 associated GATGAATACTTC CAAAC protein kinase-1 (SEQ ID NO. 5) (SEQ ID NO. 6) M-Dopa DDCNM_000790 CTTCGCCTACTTCCC CTTTGGTAGTTCCAG 55 decarboxylase CACTGCATCTTCC (SEQ ID NO. 7) (SEQ ID NO. 8) Fructose-1,6- FBP 1 NM_000507CACTGAGTACATCCA CTTCTTGTTAGCGGG 57 biphosphate GAGGAAG GTACAGdecarboxylase (SEQ ID NO. 9) (SEQ ID NO. 10) Flavin FMO5 NM001461.1GGACAGGCGACACTA CCTTTCAAAGCAGAC 53 containing ACAGG AGGTTCCmonooxygenase (SEQ ID NO. 11) (SEQ ID NO. 12) Forkhead box FOXA3NM_004497.2 TGCTGCCTCGACCAC AGTGAAATAGGGTGT 56 A3 CAC GGAGGAAG(SEQ ID NO. 13) (SEQ ID NO. 14) Fucosyl- FUT4 NM_002033.2 N/A* N/A* N/Atransferase 4 golgi GOLPH2 NM_177937.1 AGTGTGAGGAGCGAA TGTCTGGGACTTGCT53 phosphoprotein TAGAAGAG GTTACC 2 (SEQ ID NO. 15) (SEQ ID NO. 16)lysozyme LYZ NM_000239.1 GACCTAGCAGTCAAC CCATTCCCAATCTTT 53 (renalATGAAGG TCAGAGTTC amyloidosis) (SEQ ID NO. 17) (SEQ ID NO. 18)phospholipase PLCL2 NM_015184.2 CCATCAAGGAAGTGA ATATATGACGGAAAA 56C-like 2 GAACAGG CGCACAATC (SEQ ID NO. 19) (SEQ ID NO. 20) ribonuclease,RNAse4 NM_194430 GCAGAGGACCCATTC CGCAGGAATCGCTGG 57 RNase A family,ATTGC TAC 4 (SEQ ID NO. 21) (SEQ ID NO. 22) Trefoil TFF1 NM_003225CCCCGTGAAAGACAG CGTCGATGGTATTAG 53 factor 1 AATTGTG GATAGAAGC(SEQ ID NO. 23) (SEQ ID NO. 24) Trefoil TFF3 NM_003226.2 TCTGGGAGCTTGACAGGATTGTTTGCTTGG 56 factor 3 AAGGC GGAAGG (SEQ ID NO. 25) (SEQ ID NO. 26)

1.-17. (canceled)
 18. A non-endoscopic method of screening for Barrett'sesophagus (BE) in a subject comprising: obtaining a sample of cells,including columnar mucosa cells and specialized columnar mucosa cells,from the subject by retrieving a swallowable device from the subjectthat has been swallowed by the subject, the swallowable devicecomprising an abrasive material configured to collect at least somecolumnar mucosa cells and at least some specialized columnar mucosacells in the sample of cells; detecting a biomarker in the sample ofcells; and differentiating between the columnar mucosa cells and thespecialized columnar mucosa cells in the sample of cells by detectingthe biomarker in the specialized columnar mucosa cells.
 19. The methodof claim 18, wherein the specialized columnar mucosa cells areesophageal cells.
 20. The method of claim 19, wherein detecting thebiomarker in esophageal specialized columnar mucosa cells is indicativeof the subject having BE.
 21. The method of claim 18, wherein thecolumnar mucosa cells are gastric cells.
 22. The method of claim 18,wherein the biomarker is Trefoil factor 3 (TFF3).
 23. The method ofclaim 18, wherein the subject does not present with BE lesions.
 24. Themethod of claim 18, wherein the swallowable device comprises a capsulesponge.
 25. The method of claim 18, wherein the specificity andsensitivity of the method of screening for BE are about 80% and about65% respectively.
 26. The method of claim 18, wherein the specificityand sensitivity of the method of screening for BE are about 94% andabout 78% respectively.
 27. The method of claim 22, wherein detectingTFF3 comprises detecting an antibody that specifically binds to TFF3 inan immunoassay of the sample of cells.
 28. The method of claim 22,wherein detecting TFF3 comprises immunohistochemically staining thesample of cells.
 29. The method of claim 18, further comprising stainingthe sample of cells with an Alcian Blue stain to confirm diagnosis ofBE.
 30. The method of claim 18, wherein the abrasive material comprisespolyurethane.
 31. The method of claim 18, wherein the size andabrasiveness of the material is configured to sample substantially theentire esophageal surface of the subject.
 32. The method of claim 18,wherein the abrasive material of the swallowable device is digestible.33. The method of claim 32, further comprising a digestible retrievalcord coupled with the abrasive material, wherein the retrieval cord isconfigured to digest at a slower rate than the abrasive material. 34.The method of claim 27, further comprising: differentiating between thecolumnar mucosa cells and the specialized columnar mucosa cells in thesample of cells by detecting the antibody that specifically binds toTFF3 in the specialized columnar mucosa cells.
 35. The method of claim28, further comprising: differentiating between the columnar mucosacells and the specialized columnar mucosa cells in the sample of cellsby detecting TFF3 in the specialized columnar mucosa cells.